Metabarcoding of freshwater eDNA: sediment from oxbow
Environmental DNA was extracted from 1 g sediment of each replicate sample (a total of 3 g per site) using the DNeasy PowerLyzer PowerSoil DNA isolation kit (Qiagen, Hilden, Germany) according to the manufacturer's protocol. Prior to the kit, sediment samples were pre-washed with three washing solutions to improve the success of DNA amplification by PCR (Danovaro, 2010). PCR amplifications of the hyper-variable loop V9 of the 18S rDNA gene was performed with the 2X VWR Red Taq DNA polymerase Master Mix (VWR) and the forward/reverse primer-pair 1389F and 1510R (Amaral-Zettler et al., 2009).